EXIT is used to EXIT the DIALOG mode and return to the
possible to EXIT the DIALOG mode also by typing E on the keyboard.MAIN>. It has no analog in command sentences. It is
IMAGE MENU ON
OFF
MENU turns off MENU and makes the screen for molecular image larger. Menu can be obtained again by picking the area above the string MAIN displayed at the left top of the displayed viewport. Command sentences send to the main command interpreter are [IMAGE MENU ON] for getting menu to the screen and [IMAGE MENU OFF] for removing menu from the screen.
IMAGE OVER FALSE
RE_DRAW redraws the 3-dimensional objects (except MAP(s))
IMAGE MAP OVER
RE_MAP redraws the MAP(s) centered at the current IMAGE CENTER.
IMAGE STEREO ON
OFF
STEREO toggles the STEREO ON or OFF.
> inquire file_name "PLOT FILE NAME:" > open unit 99 file file_name write_enable > image unit 99 plot on initialize > image over false map over > image plot off > close unit 99
Creates a plot file of the current IMAGE. The name of the plot file is INQUIRED by the prompt "PLOT FILE NAME" and should be typed in.
IMAGE CENTER ATOM int1
Centers the image to the position of the last picked atom.
An atom is PICKED, when the cursor is placed on its IMAGE location and a mouse button is pressed.
IMAGE HISTORY INITIALIZE
HIS_ERAS empties the history array (set the counter of atoms present to zero and deletes all history images).
IMAGE HISTORY DROP
Drops the last PICKED atom from the HISTORY list.
!5 HIS_CONT !HISTORY CONTINUE ON / TRUE ! OFF / FALSE ! !Toggles the HISTORY CONTINUE flag ON or OFF. It's used when !HISTORY DISTANCE, ANGLES or DIHEDRALS are displayed. When !the CONTINUE flag is OFF only the last 2/3/4 picked atoms !are used to display the history distance, angle or dihedral. !When the CONTINUE flag is ON all distances, angles or !dihedral angles among consecutive atoms in history list are !displayed.
IMAGE HISTORY DISTANCE
Displays DISTANCE among last two PICKED atoms and connects them with the white history line.
IMAGE HISTORY ANGLE
Displays the ANGLE among the last 3 PICKED atoms and connects them with the white history line.
IMAGE HISTORY DIHEDRAL
Displays the DIHEDRAL angle among the last 4 PICKED atoms and connects them with the white history line.
IMAGE HISTORY INTERNAL
Displays DISTANCE, ANGLE and DIHEDRAL information of last 4 PICKED atoms. The CONTINUE flag does not affect displaying of internal coordinate information.
IMAGE HISTORY NEIGHBOUR his_neigh
Finds the NEIGHBOURS of the last PICKED atom. The neighbours are atoms closer than the specified distance real, at least 3 covalent bonds away from the last picked atom and are included in the key 'image'. The distance criterion is stored in the variable name 'his_neigh'. The default value is 4.0A and can be SET with a
MAIN> SET VARIABLE his_neigh real
command sentence and its value can be SHOWN with a
MAIN> SHOW VARIABLES his_neigh
IMAGE HISTORY RAMACHANDRAN
HIS_RAMA sets a cross into Ramachandran plot when it is displayed as part of the GRAPH object number 1. It is enough to PICK any atom of the desired residue and then hit HIS_ARMA. The program finds the required atoms alone (-C N CA C +N).
The modeling functions (RT_ANGLE, RT_CHAIN, RT_DIHED, ROTATE, TRANSLATE, ROT_TRAN, MOV_DIST, MV_6_INT) activate OBJECTS for interactive spatial modifications of molecular geometry and assign DIALS to them. After activating an OBJECT the IMAGE has to be redrawn (RE_DRAW). Most of them consist of more than one command sentence or even call some external command files. (So don't get confused when looking into the file INPUT.COP). The required data are transferred to the command files via MAIN VARIABLES.
>SET VARIABLE iatom1 int1 VARIABLE iatom2 int2 VARIABLE iatom3 - int3 VARIABLE iobj1 int4] >@MAIN$U:ANGLE.ROTA
Defines an ANGLE OBJECT. Takes the last 3 atoms from the HISTORY list.
> SET VARIABLE iatom1 int1 VARIABLE iatom2 int2 VARIABLE iatom3 - int3 VARIABLE iatom4 int4 VARIABLE iobj1 int5 > @MAIN$U:DIHED.ROTA]
Defines a DIHEDRAL OBJECT. Takes the last 4 atoms from the HISTORY list.
RT_CHAIN activates rotation of all BONDS between the last 2 PICKED atoms. When the chain is to long or there are rings in the system OB_REJECT should be done by the user in order to avoid possible misdefinitions. MAIN is able to checking only each separate bond rotation. When there are more bonds to be rotated in the chain and one is not allow to rotate, some error messages will appear.
RT_CHAIN calls in a loop a variety of command files, for each rotatable bond one. After each 8th bond, the DIAL WRITE sentence is automatically done. The last DIAL definition should be saved by the user in order to keep it on the DIAL definitions stack.
> SET VARIABLE iatom1 atom-num1 VARIABLE iatom2 atom-num2 VARIABLE iobj1 inte > MAIN$U:BOND.DIST
Moves (translates) the molecule of the last PICKED atom. in the direction of the vector connecting the last two PICKED atoms.
Activates 3 BOND and 2 ANGLE rotations and 1 DISTANCE movement. It is the INTERNAL (relative) coordinate way of the ROTATION and TRANSLATION (ROT_TRAN) function that is applied in absolute (cartesian) coordinate space. The 6 last PICKED history atoms are required. The DIAL set is saved automatically.
ROTATES the molecule of the last PICKED atom around the last picked atom.
TRANSLATES the molecule of the last PICKED atom.
Combines ROTATION and TRANSLATION of the molecule of the last PICKED atom. The center of rotation is defined at the position of the last PICKED atom. The DIAL set is saved automatically.
> SET INVERSE atom-num1 atom-num2
Interchanges the positions of the 2 side chains attached to a single atom. In other words: inverses chirality of the common neighbour of the last 2 PICKED atoms.
Controls the DIAL definitions.
Set dials to their INITIAL (default) definition. (image center translation, scaling, rotation and clipping)
Makes a backup of the current DIAL definition to the memory.
> SET DIAL 1 WRITE
Restores a DIAL set definition from the memory and increases current dial set counter for one.
> SET DIAL 1 VIEW
Assigns DIALS to VIEW parameters as scaling of screen, stereo angle, distances from viewer position to the center, character scale.
Drops all of saved (backuped) DIAL sets from the memory and initialize dials.
OB_START
> OBJECT int SET INIT
OB_REJEC
>OBJECT int SET TRUE
OB_ACCEP
>OBJECT int SET FALSE
These commands affect all activated OBJECTS. They are either returned to their initial position (OB_START) or reject the changes completely (OB_REJEC) or accepts (OB_ACCEP) them and change the atom coordinates. By OB_REJEC and OB_ACCEP the complete image is redrawn.
> DELETE BOND atom-num1 atom-num2
A covalent BOND between the last 2 PICKED atoms can be DELETED or created (JOIN).
> JOIN atom-num1 atom-num2
A covalent BOND between the last 2 PICKED atoms can be DELETED or created (JOINED).
!BON_INCR increases order of a bonds (creates a double bond out of a single one) !BON_DECR decreases order of a bonds (creates a single bond out of a double one)
> make atom coordinate 3*real > image color 222 select atom number atom-num1 end atom cross
MAKES an ATOM with the name X at the current image CENTER position and displays it as a CROSS.
> delete atom select atom number atom-num1 end
DELETES the last PICKED atom. Since this is a very risky operation the user is asked once more to confirm the DELETION.
> make pair atom-num1 atom-num2
MAKES a PAIR from the last 2 PICKED atoms.